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larssnip / HumGut

A healthy human gut genome collection
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Build a kraken2 db using HumGut #1

Open antgomo opened 3 years ago

antgomo commented 3 years ago

Hi, want to know ho to deal with your HumGut file from

http://arken.nmbu.no/~larssn/humgut/

Thanks

larssnip commented 3 years ago

Hi,

There are actually two files: HumGut.tar.gz is a compressed tar-archive with a fasta-file for each genome (~18GB). Click on it and download it, then uncompress and untar.

HumGut.csv is a text file with a table of metadata for the genomes in the first file.

When it comes to building a kraken2 database from this, you also need the taxonomy-files listed at the end of the page you are linking to. I have actually prepared better descriptions of this, but haven't had time to put it out here. Will do so as soon as possible now!

antgomo commented 3 years ago

Ok, thanks Lars!

larssnip commented 3 years ago

Hi again,

I updated the GitHub site this weekend, there should now be some suggestions on how to make kraken2 database.

LS

From: antgomo @.> Sent: mandag 12. april 2021 10:39 To: larssnip/HumGut @.> Cc: Lars-Gustav Snipen @.>; Comment @.> Subject: Re: [larssnip/HumGut] Build a kraken2 db using HumGut (#1)

Ok, thanks Lars!

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